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Yorodumi- PDB-5w36: Crystal structure of the RNA polymerase domain (RPD) of Mycobacte... -
+Open data
-Basic information
Entry | Database: PDB / ID: 5w36 | ||||||
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Title | Crystal structure of the RNA polymerase domain (RPD) of Mycobacterium tuberculosis primase DnaG in complex with a double-stranded DNA oligomer with a 6-nucleotide overhang | ||||||
Components |
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Keywords | TRANSFERASE / DNA replication / replisome / TOPRIM fold / DNA binding | ||||||
Function / homology | Function and homology information DNA primase DnaG / DNA primase activity / primosome complex / DNA replication, synthesis of primer / DNA-directed RNA polymerase complex / DNA binding / zinc ion binding / plasma membrane / cytoplasm Similarity search - Function | ||||||
Biological species | Mycobacterium tuberculosis (bacteria) synthetic construct (others) | ||||||
Method | X-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.46 Å | ||||||
Authors | Hou, C. / Tsodikov, O.V. | ||||||
Citation | Journal: Biochemistry / Year: 2018 Title: Structures of the Catalytic Domain of Bacterial Primase DnaG in Complexes with DNA Provide Insight into Key Priming Events. Authors: Hou, C. / Biswas, T. / Tsodikov, O.V. | ||||||
History |
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-Structure visualization
Structure viewer | Molecule: MolmilJmol/JSmol |
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-Downloads & links
-Download
PDBx/mmCIF format | 5w36.cif.gz | 139.5 KB | Display | PDBx/mmCIF format |
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PDB format | pdb5w36.ent.gz | 105.7 KB | Display | PDB format |
PDBx/mmJSON format | 5w36.json.gz | Tree view | PDBx/mmJSON format | |
Others | Other downloads |
-Validation report
Arichive directory | https://data.pdbj.org/pub/pdb/validation_reports/w3/5w36 ftp://data.pdbj.org/pub/pdb/validation_reports/w3/5w36 | HTTPS FTP |
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-Related structure data
Related structure data | 5w33C 5w34SC 5w35C C: citing same article (ref.) S: Starting model for refinement |
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Similar structure data |
-Links
-Assembly
Deposited unit |
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1 |
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Unit cell |
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-Components
#1: Protein | Mass: 35450.410 Da / Num. of mol.: 2 Source method: isolated from a genetically manipulated source Source: (gene. exp.) Mycobacterium tuberculosis (strain ATCC 25618 / H37Rv) (bacteria) Strain: ATCC 25618 / H37Rv / Gene: dnaG, Rv2343c, MTCY98.12c / Production host: Escherichia coli BL21(DE3) (bacteria) / Strain (production host): BL21(DE3) References: UniProt: P9WNW1, Transferases; Transferring phosphorus-containing groups; Nucleotidyltransferases #2: DNA chain | | Mass: 4167.704 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) synthetic construct (others) #3: Chemical | ChemComp-SR / | #4: Water | ChemComp-HOH / | |
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-Experimental details
-Experiment
Experiment | Method: X-RAY DIFFRACTION / Number of used crystals: 1 |
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-Sample preparation
Crystal | Density Matthews: 2.72 Å3/Da / Density % sol: 54.7 % |
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Crystal grow | Temperature: 294 K / Method: vapor diffusion, hanging drop / pH: 6 Details: 100 mM sodium citrate pH 6.0, 5% w/v PEG 4000 and 5 mM SrCl2 |
-Data collection
Diffraction | Mean temperature: 100 K |
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Diffraction source | Source: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å |
Detector | Type: RAYONIX MX300-HS / Detector: CCD / Date: Mar 25, 2017 |
Radiation | Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray |
Radiation wavelength | Wavelength: 1 Å / Relative weight: 1 |
Reflection | Resolution: 2.45→50 Å / Num. obs: 27849 / % possible obs: 96.2 % / Redundancy: 2.7 % / Net I/σ(I): 23 |
-Processing
Software |
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Refinement | Method to determine structure: MOLECULAR REPLACEMENT Starting model: 5W34 Resolution: 2.46→35 Å / Cor.coef. Fo:Fc: 0.946 / Cor.coef. Fo:Fc free: 0.92 / SU B: 11.993 / SU ML: 0.262 / Cross valid method: THROUGHOUT / ESU R: 0.48 / ESU R Free: 0.296 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
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Solvent computation | Ion probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å | ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
Displacement parameters |
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Refinement step | Cycle: 1 / Resolution: 2.46→35 Å
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Refine LS restraints |
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